tbuckley/cabot-search huggingface dataset:
Use of secondary subgroup analysis of clinical trials across solid malignancies.
Authors: Marah Alzubi, Nada Wael Odeh, Muntaser A.l. Zyoud, Yazan Hamadneh, Jawad Alrawabdeh, Samer A.l. Hadidi
Journal: Journal of Clinical Oncology (2023)

e13618 Background: The use of secondary (subgroup) analyses in medical literature is increasing. Findings from subgroup analyses may be misleading given they are observational in nature and do not resemble a randomized comparisons. Our study aimed to characterize the use of post hoc subgroup analysis in interventional clinical trials across solid malignancies. Methods: We searched OVID database for articles subgroup analyses from the year 2000 until Feb 15, 2022. Some of the used search terms were post-hoc, subgroup, secondary, cancer, tumor, breast, colorectal. 11641 articles were screened to include all secondary analyses of interventional solid tumor clinical trials. We excluded original trials, secondary analyses of cohort/observational studies. Results: Our final analysis included 1491 articles. Most studied malignancy was gastrointestinal cancers (22.6%), followed by genitourinary cancers (21%), and breast cancer (19%). The number of papers published per year increased steadily over the years with a peak in 2021 (16% of all articles). About 78% of articles reported receiving funding, with 40% reporting pharma-related funding. 29% of articles reported the usage of a medical writer. 55% of articles reported that authors had conflicts of interest (COI). Pharma-related funding was significantly associated with usage of a medical writer (p &lt; 0.001). The mean percentage of authors with COI was 31.8 ± 0.95%. Articles that reported usage of a medical writer had a higher percentage of authors with COI (p &lt; 0.0001). Women represented 32.7% and 25.9% of first and last authors, respectively. About 44% of both first and last authors resided in North America. Half of the articles explicitly indicated that they were secondary analyses in their titles. [Table]. Conclusions: Our study indicated that the use of secondary subgroup analysis in solid malignancies clinical trials is increasing. Half of the studies did not clarify the nature of them being secondary analyses in the title. Given their increased use, caution must be entertained when interpreting the results of secondary analysis. [Table: see text]
Clinical outcomes of patients with metastatic breast cancer treated with eribulin: A real-world evidence study from China.
Authors: Xi Yan, Lan Chen, Ping He, Ting-Lun Tian, Xiaorong Zhong, Ting Luo
Journal: Journal of Clinical Oncology (2023)

e13126 Background: Eribulin is a novel synthetic analog of halichondrin B that acts as a microtubule inhibitor and inhibits the G2-M growth phase. Eribulin was approved for metastatic breast cancer (MBC) based on the landmark phase 3 EMBRACE trial (Cortes et al, Lancet 2011; NCT00388726); however, only a small number of Asian patients were included in that trial. Therefore, in this real-world study, we retrospectively assessed the clinical outcomes of Chinese patients with MBC who received eribulin. Methods: Adult patients with MBC who received eribulin as several lines of therapy were retrospectively analyzed. Socio-demographic, clinical, pathology, imaging, and therapy records were reviewed. Progression-free survival (PFS) and tumor response were evaluated. Results: A total of 85 patients were included. The median age was 45 years (range, 21–63). Eribulin was used as a first, second, third, and fourth or more chemotherapy agent in 13 (15.3%), 16 (18.8%), 11 (12.9%) and 45 (52.9%) of patients with MBC, respectively. Eribulin was monotherapy in 32.9% of patients; eribulin plus anti-HER2 targeted therapy was used in 9.4% of patients; eribulin plus immunotherapy was used in 5.9% of patients; eribulin plus other chemotherapy was used in 36.5% of patients, and eribulin plus antiangiogenic therapy was used in 9.4% of patients. The objective response rate (ORR) was 28.2% overall. By number of lines of therapy, the first-line ORR was 38.5% and the second-line ORR was 37.5%. On subgroup analysis, ORR of patients with liver metastasis and lung metastasis was 43.9% and 38.6 %, respectively. By molecular classification, the ORR of patients with HR+/HER2− disease was 66.7%; among patients with HER2+ disease, 32.6%; and among patients with triple-negative BC, 13.3%. The 6-month PFS rate was 33.6% overall. By number of lines of therapy, the 6-month PFS rate among patients who received eribulin as first-line treatment was 67.7% and among patients who received eribulin as second-line treatment, 38.3%. Among patients who received eribulin monotherapy, the 6-month PFS rate was 21.4% and among patients who received eribulin combination therapy, 41.2%. No adverse reactions related to neutrophils were reported. Conclusions: This real-world retrospective study suggests that eribulin was effective in Chinese patients with MBC with a range of prior lines of chemotherapy, supporting the use of eribulin in the treatment of Chinese patients with MBC.
Exosome-based delivery of microRNAs to confer adriamycin-resistance to sensitive cells through modulating the immune- and metabolism-related gene PTEN in HER2-negative breast cancer.
Authors: Sujin Yang, Jinhai Tang
Journal: Journal of Clinical Oncology (2023)

e12518 Background: Anthracycline-based chemotherapy is frequently used to treat breast cancer. However, acquired drug-resistance remains a challenge for successful treatment. Recent evidence suggests that in addition to increased tumor cell resistance, modifications in the tumor immune microenvironment (TIME) consistently contribute to the development of chemo-resistance. Methods: TIME scores and tumor-infiltrating immune cells (TICs) scores were used to investigate clinicopathological characteristics and gene transcriptome profiling of 142 HER2-negative breast cancer patients who received anthracycline-based chemotherapy. Exosomes isolated from MCF/7-ADR (ADR-exos) and MCF/7-S (S-exos) cell lines were characterized. MiRNA microarray and TMT mass spectrometry analysis were used to identify differentially expressed miRNA and its target genes. The ability of ADR-exos to transfer drug-resistance mediated by miR-222 was assessed by immunofluorescence assay, flow cytometry and qRT-PCR. We optimized the conditions to load miR-222 mimic (or inhibitor) into exosomes produced by HBL-100 cells (H-exos). The influence of miR-222 inhibitor-containing exosomes on the downstream pathway of miR-222 and the potential therapeutic effects both in vitro and in vivo were evaluated. Results: Firstly, we discovered the complicated and heterogenous TICs subtypes and their unique biological behaviors in HER2-negative breast cancer. Gene set variation analysis (GSVA) was used to quantify 85 differentially expressed immunologic signature gene sets and 7202 corresponding immune-related genes. Using miRNA microarray analysis and TMT mass spectrometry, 45 differentially expressed immune-related proteins affected by the miR-222 level were identified, particularly PTEN, a well-known tumor suppressor factor. Furthermore, we successfully established miRNA mimic/inhibitor-containing exosomes to explore the individual function of exosomal miR-222 in promoting adriamycin-resistance both in vitro and in vivo. Conclusions: HER2-negative breast cancer patients own unique TIME subtypes, leading to different outcomes of chemotherapy. We exhibit the potential applications of miR-222-mimic/inhibitor-containing exosomes for reversing chemo-resistance. Adriamycin-resistant cells can transmit drug-resistance to sensitive cells via delivering miR-222 by modulating the immune- and metabolism-related target gene PTEN both in vitro and in vivo without interference from other relevant drug-resistance factors in exosomes. Therefore, miR-222-containing exosomes as well as the target gene PTEN may be a promising biomarker to predict the chemo-resistance and tumor immunomodulatory effects of Anthracycline-based chemotherapy in HER2-negative breast cancer patients.
Effect of tumor microenvironment on chemotherapy response of patients with triple-negative breast cancer receiving neoadjuvant chemotherapy.
Authors: Jae-Joon Kim, Dongjin Kim, Yeuni Yu, Ki Sun Jung, Yun Hak Kim
Journal: Journal of Clinical Oncology (2023)

590 Background: Triple-negative breast cancer (TNBC) is a breast cancer subtype that has poor prognosis and exhibits a unique tumor microenvironment, including the corresponding immunological environment. Analysis of the tumor microbiome has indicated a relationship between the tumor microenvironment and treatment response. Therefore, we attempted to reveal the role of the tumor microbiome in patients with TNBC that were receiving neoadjuvant chemotherapy. Methods: We collected TNBC patient RNA-seq samples from the Gene Expression Omnibus (GEO; n of pathological complete response [pCR] = 38, n of residual disease [RD] = 50) and extracted microbiome count data using Kraken2 and Bracken. Differential and relative abundance were estimated with linear discriminant analysis effect size (LEfSe). We calculated the immune cell fraction with CIBERSORTx and conducted survival analysis using the Cancer Genome Atlas patient data (n = 115). Correlations between the microbiome and immune cell compositions were analyzed and a prediction model was constructed to estimate drug response using random forest (RF) and support vector machine (SVM). Results: Among the drug response group, the beta diversity varied considerably; consequently, 20 genera and 24 species were observed to express a significant differential and relative abundance using LEfSe analysis. The drug response prediction model accuracy exhibited 76.47 and 88.24 percent in RF and SVM, respectively; specifically, Pandoraea pulmonicola and Brucella melitensis were found to be important features in determining drug response. In correlation analysis, Geosporobacter ferrireducens, Streptococcus sanguinis, and resting natural killer cells were the most correlated factors in the pCR group, whereas Nitrosospira briensis, Plantactinospora sp. BC1, and regulatory T cells (Tregs) were key features in the RD group. Further, M2 macrophages and Brucella showed significant differences in survival between the pCR and RD groups (p &lt; 0.05). Conclusions: Our study demonstrated that the microbiome analysis of tumor tissue can predict chemotherapy response of patients with TNBC receiving neoadjuvant chemotherapy. Further, the immunological tumor microenvironment may be impacted by the tumor microbiome, thereby affecting the corresponding survival and treatment response.
Efficacy of oral selective estrogen receptor degraders (SERD)s in the treatment of estrogen receptor positive (ER+), HER2-negative metastatic breast cancer (MBC): A stratified analysis of the ESR1 wild type (wt) and mutant (mt) subgroups.
Authors: Joseph J Zhao, Nicky Wong Zhun Hong, Dominic Wei Ting Yap, Rebecca Jia Min Ong, Raghav Sundar, Joline Si Jing Lim, Shaheenah S. Dawood
Journal: Journal of Clinical Oncology (2023)

1096 Background: Oral SERDs are a novel drug class developed to counteract endocrine resistance due to ESR1 mutations. Several SERDs have emerged from phase 2 and 3 trials, and the FDA has most recently limited approval for Elacestrant to patients with ESR1mt tumours despite PFS benefit in the overall population. Questions remain on whether patients with ESR1wt tumours stand to benefit from SERDs. We conducted an IPD meta-analysis of the trials EMERALD, SERENA2, ACELERA and AMEERA3 to compare survival outcomes of SERDs in the 2nd or 3rd line setting against endocrine therapy (ET), using KMSubtraction to unveil HRs of unreported ESR1wt subgroups from AMEERA3 and EMERALD. Meta-analysis results were stratified by ESR1 status. Methods: RCTs investigating the efficacy of novel SERDs versus ET for ER+, HER2- MBC, and which reported the Kaplan Meier (KM) plots of progression free survival (PFS) were selected after a systematic search of Embase and PubMed from inception until January 21,2023. A graphical reconstructive algorithm was applied to estimate time-to-event outcomes from reported KM plots in all overall and reported subgroup cohorts, deriving IPD. A bipartite matching algorithm, KMSubtraction was used to subtract patients in the reported subgroup from the overall cohort, to derive survival data for unreported ESR1wt subgroups. An IPD meta-analysis was then performed, pooling data by ESR1 mutation. Results: A total of 1216 patients were included in this analysis. In the pooled analysis of the overall cohort, PFS benefit was observed with SERDs compared to treatment of physician's choice (TPC) (HR 0.787, 95%CI 0.683-0.908, p&lt;0.001). In the ESR1mt subgroup SERDs demonstrated improved PFS (HR 0.557, 95%CI 0.440-0.705, p&lt;0.001) compared with TPC. In the ESR1wt subgroup, SERDs demonstrated no significant PFS benefit (HR 0.948, 95%CI 0.790-1.137, p=0.565) when compared to TPC. KMSubtraction was implemented on AMEERA3 to reveal survival data in ESR1wt subgroup. Amcenestrant revealed no significant PFS difference in the ESR1wt population (HR 1.197, 95% CI 0.857-1.670, p=0.291) when compared to ET. Additionally, a separate analysis of EMERALD was performed using KMSubtraction to derive survival data of the ESR1wt subgroup comparing Elacestrant vs Fulvestrant. No significant PFS difference was observed between the 2 agents in the ESR1wt population (HR 0.832, 95% CI 0.587-1.178, p=0.299). Conclusions: Our results suggest that PFS benefit in the overall population is mainly driven by the ESR1mt subgroup. These findings are in line with the recent FDA approval of Elacestrant for patients with ESR1mt tumours. [Table: see text]
Whole-genome sequencing based assessment of HER2 focal amplification for precision oncology of breast cancers.
Authors: Ryul Kim, Joonoh Lim, Hansol Park, Seongyeol Park, Baek-Lok Oh, Sangmoon Lee, Ji-Yeon Kim, Seok Jin Nam, Seok Won Kim, Jeong Eon Lee, Jonghan Yu, Ji In Ryu, Jeong Seok Lee, Minsuk Kwon, Jeongmin Lee, Yeon Hee Park, Young Seok Ju
Journal: Journal of Clinical Oncology (2023)

609 Background: Focal oncogene amplification confers a growth advantage to tumor cells and drives cancer evolution. Herein, we aimed to explore focally amplified HER2 in breast carcinomas. Methods: We performed whole genome sequencing (WGS) and whole-transcriptome sequencing (WTS) in 787 breast cancer samples. HER2 focal amplification was defined as having a segment length less than 3Mbp and ≥4 higher copy number than the surrounding region. Results: Most of the patients were premenopausal women (n = 574, 72.9%) with a median age of 37 (range 21-76) years. We identified 57 (58.8%) and 27 (5.0%) samples with HER2 focal amplification in HER2-positive (n = 97) and even HER2-negative (n = 536) by immunohistochemistry (IHC) and in-situ hybridization (ISH) according to ASCO guideline for breast cancer, respectively. Regardless of HER2-positivity, HER2 focal amplification was significantly associated with higher HER2 RNA expression. Among 28 patients who received six cycles of docetaxel/carboplatin/trastuzumab/pertuzumab neoadjuvant therapy followed by curative surgery, 21 patients had HER2 focal amplification and 14 (66.7%) achieved pathologic complete remission (pCR). Intriguingly, all patients without HER2 focal amplification (n = 7) failed to achieve pCR. HER2 focal amplification showed enrichment of TP53 mutations (OR 0.245, q &lt; 0.001), but was mutually exclusive with GATA3 mutations (OR 2.82, q = 0.055). The mutational spectrums suggested that the activity in APOBEC family of cytidine deaminases were responsible for the somatic single-nucleotide variants of breast cancer with HER2 focal amplification. Compared to samples without HER2 focal amplification, samples with HER2 focal amplification were less likely to have defective homologous recombination DNA repair pathway. HER focal amplifications were closely associated with various types of structural variations. Translocation partners of HER2 were widespread across the entire genome with notable exceptions on chromosome 2, and most of them were close to super-enhancers implying enhancer hijacking as one of mechanisms of HER2 overexpression. Breast cancers with or without HER2 focal amplification showed distinct RNA expression patterns. Notably, activity of genes involved in doxorubicin-resistance and AKT1 signaling were significantly associated with HER2 focal amplification. Conclusions: Our analysis demonstrates that WGS enables better classification of the HER2 amplification status in breast cancer than IHC with ISH, suggesting WGS as a sensitive tool for screening breast cancers for anti-HER2-targeted therapies.
Magnetic resonance imaging tumor regression shrinkage patterns during neoadjuvant chemotherapy versus neoadjuvant immunochemotherapy in triple-negative breast cancer (NeoMDSS-TN-SP): A nonrandomized, prospective cohort study.
Authors: Liulu Zhang, Jiachen Zou, Yuanqi Chen, Xinjian Yan, Kun Wang
Journal: Journal of Clinical Oncology (2023)

e12601 Background: Previous studies have shown that the tumor regression shrinkage pattern (SP) of triple-negative breast cancer (TNBC) during neoadjuvant chemotherapy (NAC) is more likely to present with concentric shrinkage (CS), which is associated with a pathological complete response (pCR). Since immunotherapy and chemotherapy have different antitumor mechanisms, it is reasonable to believe that there may be different SPs between neoadjuvant immunochemotherapy (NAIC) and NAC. This NeoMDSS-TN-SP prospective study aimed to investigate whether tumor SPs differed between NAIC and NAC in TNBC, as well as to calculate the correlation between SP and efficacy. Methods: In this prospective, single-center, nonrandomized cohort study, eligible patients with stage II-III TNBC received NAIC or NAC and underwent MRI at baseline, after the first cycle of neoadjuvant therapy, and preoperatively. Based on the MRI after the first cycle, the tumor SPs were grouped into three categories: CS, diffuse decrease, and no change or enlargement. The primary end point was the difference in SP between the two treatment groups. Secondary endpoints included the correlation between SP and treatment efficacy. This study is registered with ClinicalTrials.gov, number NCT04909554. Results: Ninety-nine patients were enrolled from January 2019 to July 2021; 65 received NAC and 34 received NAIC. Baseline characteristics were similar between the two groups. More patients in the NAIC group achieved pCR after surgery than in the NAC group (82.4% vs. 44.6%, p=0.0003). In the NAC group, more patients showed CS (53.8%), and patients with the CS pattern had a significantly higher pCR rate than those with diffuse decrease or no change/enlargement (65.7% vs. 21.7% vs. 14.3%, p=0.0007). In the NAIC group, although a higher proportion of patients showed diffuse decrease (67.6%), all three SP categories had relatively high pCR rates, so pCR was not correlated with SP (85.7% vs. 82.6% vs. 75.0%, p=0.9029). Conclusions: This is the first study to investigate the tumor regression SP of NAIC in TNBC patients. Compared to traditional chemotherapy, NAIC was more prone to diffuse regression, but the relatively high pCR rates had no correlation with the SPs during neoadjuvant therapy. Clinical trial information: NCT04909554 . [Table: see text]
Defendor special: Interim analysis of TCHP with primary empegfilgrastim prophylaxis (long-acting G-CSF) for treatment outcomes in early HER2+ breast cancer.
Authors: Lyudmila Zhukova, Tansylu Ibragimova, Inna Ganshina, Daria Filonenko, Irina Sorokina
Journal: Journal of Clinical Oncology (2023)

e12586 Background: TCHP is the standard regimen for neoadjuvant therapy (NAT) of HER2-positive early breast cancer (HER2+ eBC) and requires primary G-CSF prophylaxis (PP). Pathological complete response (pCR) after NAT reflects better pts outcomes. Long-acting G-CSF presents more balanced neutrophils (NEU) count vs short G-CSF. Preclinical data show tumor-associated neutrophils (TANs) as anti-tumor effector cells in eBC. There are limited data on the clinical benefit of TCHP in the subset of patients with HER2 amplification by ISH in the low-moderate of HER2 protein expression. This sub-group analysis of multicenter prospective study was designed to evaluate the pCR after TCHP with PP by empegfilgrastim (E) or filgrastim (F) in pts with HER2+ eBC. Methods: HER2+ eBC pts (n=199) with II-III stages are getting NAТ: 6 docetaxel/ carboplatin/ trastuzumab + pertuzumab + empegfilrastim/ filgrastim (TCHP+E/F). Short G-CSF (F) uses according to routine clinical practice, long-acting G-CSF (E) - 24h after each NAT cycle. This descriptive analyse were performed for pts who completed the whole NAT regimen. The study endpoints: pCR (ypT0/is, ypN0) in intention-to-treat (ITT) population and according to HER2 status: 3+ vs 2+ ISH positive (+). ClinicalTrials.gov No NCT04905329. Results: At the data cut-off (01’2023) 199 pts with HER2+ BC completed planned NAT and surgery (71 pts – TCHP+E; 128 pts – TCHP+F). pCR rate according to HER2 status and in ITT population in 2 G-CSF groups is presented. In TCHP+E group pCR rate exceeds KRISTINE trial data despite a more enriched pts’ population with poor prognosis (34% pts with IIIB - IIIC vs 17% pts in KRISTINE trial) while TCHP+F showed comparable results with historical control. The superior pCR rate under PP with E was also observed in HER2 (3+) pts sub-group vs PP with F. However, in HER2 (2+ ISH+) the results are similar in 2 G-CSF groups. The mature data are awaited. Conclusions: TCHP+E shows superior pCR rate vs TCHP+F in the ITT and HER2 (3+) population. The obtained results affirm data of preclinical research on the ability of G-CSF to switch tumor immunity from “cold” to “hot” in the eBC. We assumed that balanced NEU count under long-acting G-CSF stimulation enhances TANs infiltration is increasing therapy efficiency. In HER2 (2+ ISH+) population pCR results were comparable in 2 G-CSF groups. Discrepancies between gene amplification and protein overexpression resulted in declined amount of HER2-inhibitors-HER2 receptor active complexes. It can be TANs failure to kill anti-HER2-antibody-opsonized cancer cells by a trogoptosis. Our hypothesis requires further confirmation with translational research. Clinical trial information: NCT04905329 . [Table: see text]